Abstract
Background. CRISPR/Cas systems loci are one of the functionally important patterns in bacterial genome which perform the role of “adaptive immune defense” from foreign nucleic acids. The study of CRISPR/Cas systems structure in genomes of plasmids and phages provide new information about the evolution of this systems in bacterial hosts.Aims. A search of CRISPR/Cas systems structures in pCT281 plasmid from Bacillus thuringiensis subsp. chinensis strain CT-43 using bioinformatic methods.Materials and methods. Search studies using bioinformatics methods were performed with the genome of pCT281 plasmid of B. thuringiensis subsp. chinensis strain CT-43 from the RefSeq database. To search for the CRISPR/Cas system structure MacSyFinder (ver. 1.0.5) and three combined algorithms were used: CRISPRFinder; PILER-CR; CRISPR Recognition Tool (CRT). The consensus repeat sequence was generated in WebLogo 3.Results and discussion. In pCT281 plasmid we detected one locus of CRISPR/Cas system of the type I-C which contains 2 CRISPR-cassettes and 4 cas-genes located between them. The CRISPR-cassette 1 includes 10 spacers from 32 to 35 bp and 11 repeats 32bp in length. 5 spacers (33–35 bp) separated by 6 repeats 32 bp in length were detected in the CRISPR-cassette 2.Conclusions. The bioinformatic methods used in this study enable to conduct a search of CRISPR/Cas systems structures in plasmid genomes. The presence of the CRISPR-Cas locus in pCT281 plasmid confirms a possible transfer of this system from the nucleoid to this plasmid. The detected spacers provide information about phages this bacteria was encountered.
Highlights
CRISPR/Cas systems loci are one of the functionally important patterns in bacterial genome which perform the role of “adaptive immune defense” from foreign nucleic acids
Search studies using bioinformatics methods were performed with the genome of pCT281 plasmid of B. thuringiensis subsp. chinensis strain CT-43 from the RefSeq database
The CRISPR-cassette 1 includes 10 spacers from 32 to 35 bp and 11 repeats 32bp in length. 5 spacers (33–35 bp) separated by 6 repeats 32 bp in length were detected in the CRISPR-cassette 2
Summary
CRISPR/Cas systems loci are one of the functionally important patterns in bacterial genome which perform the role of “adaptive immune defense” from foreign nucleic acids. The study of CRISPR/Cas systems structure in genomes of plasmids and phages provide new information about the evolution of this systems in bacterial hosts. A search of CRISPR/Cas systems structures in pCT281 plasmid from Bacillus thuringiensis subsp. Search studies using bioinformatics methods were performed with the genome of pCT281 plasmid of B. thuringiensis subsp. The bioinformatic methods used in this study enable to conduct a search of CRISPR/Cas systems structures in plasmid genomes. For citation: Arefyeva N.A., Dzhioev Yu.P., Borisenko A.Yu., Chemerilova V.I., Vyatchina O.F., Sekerina O.A., Stepanenko L.A., Markova Yu.A., Yurinova G.V., Salovarova V.P., Pristavka A.A., Kuzminova V.A., Reva O.N., Zlobin V.I. Bioinformatic Search of CRISPR/Cas System Structures in Genome of pCT281 Plasmid of Bacillus thuringiensis subsp. Целью данной работы был поиск структур CRISPR/Cas-систем в геноме плазмиды pCT281 штамма Bacillus thuringiensis subsp. Целью данной работы был поиск структур CRISPR/Cas-систем в геноме плазмиды pCT281 штамма Bacillus thuringiensis subsp. chinensis CT-43 при помощи методов биоинформатики
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